Related papers: A typical workflow to simulate cytoskeletal system…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Actomyosin contractility is essential for biological force generation, and is well understood in highly organized structures such as striated muscle. Additionally, actomyosin bundles devoid of this organization are known to contract both in…
High-Level Synthesis allows hardware designers to create complex RTL designs using C/C++. The traditional HLS workflow involves iterations of C/C++ simulation for partial functional verification and HLS synthesis for coarse timing…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set-point. This phenomenon is often referred to as mechanical homeostasis. In contradiction…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
We introduce a mathematical model for the mechanical behaviour of the eukaryotic cell cytoskeleton. This discrete model involves a regular array of pre-stressed protein filaments that exhibit resistance to enthalpic stretching, joined at…
Actin and myosin drive many instances of force generation, deformation, and shape change in cells, tissues, and organisms. In particular, cytoskeletal actomyosin is remarkable in its adaptive architecture, responding to a host of…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
We propose a class of microstructurally informed models for the linear elastic mechanical behavior of cross-linked polymer networks such as the actin cytoskeleton. Salient features of the models include the possibility to represent…
Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network…
Brightfield time-lapse imaging is widely used in cardiac tissue engineering, yet the absence of standardized, interpretable analytical frameworks limits reproducibility and cross-platform comparison. We present an open, scalable…
The coherent Ising machine (CIM) enables efficient sampling of low-lying energy states of the Ising Hamiltonian with all-to-all connectivity by encoding the spins in the amplitudes of pulsed modes in an optical parametric oscillator (OPO).…
Exploring the intricate dynamics between muscular and skeletal structures is pivotal for understanding human motion. This domain presents substantial challenges, primarily attributed to the intensive resources required for acquiring ground…
The design and analysis of systems that combine computational behaviour with physical processes' continuous dynamics - such as movement, velocity, and voltage - is a famous, challenging task. Several theoretical results from programming…
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
The macroscopic properties, the properties of individual components and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the…
The cellular cytoskeleton is an active material, driven out of equilibrium by molecular motor proteins. It is not understood how the collective behaviors of cytoskeletal networks emerge from the properties of the network's constituent motor…
The open-source code FESTIM (Finite Element Simulation of Tritium In Materials) is a powerful user-friendly software for hydrogen transport simulations. Up to now, it was capable of addressing various hydrogen transport problems with…